[ensembl-dev] VEP installation problems - unable to install GRCh37 caches

[Cyriac Kandoth]

Hi Paul,

It is appropriate to post such a qn to dev at ensembl. If you have an issue
specifically with vcf2maf, we (mskcc) can help you at
https://github.com/mskcc/vcf2maf/issues

The latest readme for vcf2maf includes instructions for installing VEP v83
- https://github.com/mskcc/vcf2maf - I will remove these instructions in
the next few days in favor of gists. Here's a gist for installing VEP v84
with an offline cache for GRCh37 -
https://gist.github.com/ckandoth/57d189f018b448774704d3b2191720a6

~Cyriac

On Tue, Apr 19, 2016 at 4:07 AM, Paul Hatton <P.S.HATTON at bham.ac.uk> wrote:

> Apologies if this is the wrong list to post this to, but a search for this
> problem led me to this list and I can't find any mention of it in the
> archives (which sort-of suggests that I'm on the wrong list).
>
> I look after the applications base on our Linux-based HPC service at the
> University of Birmingham (UK) and we have recently established a new Centre
> for Computational Biology and hence I am asked to install much specialist
> software such as VEP. I have a great deal of experience in installing
> applications on a Linux HPC service but limited experience of these
> specialist applications, so apologies again if this is a naive question
> posted to the wrong list .... feel free to point me elsewhere if more
> appropriate ......
>
> Anyhow, I have been asked to get vcf2maf running, which depends on VEP. I
> have been unable to get a clean installation of VEP 82, 83 or 84 which I
> think is having knock-on problems to users running vcf2maf, and so I'd like
> to get VEP installed cleanly first. Whilst VEP itself build fine with
>
> cd ensembl-tools-release-84/scripts/variant_effect_predictor
> export PERL5LIB=/gpfs/apps/VEP/84:$PERL5LIB
> export PATH=/gpfs/apps/VEP/84/htslib:$PATH
> perl INSTALL.pl --DESTDIR /gpfs/apps/VEP/84 --CACHEDIR
> /gpfs/apps/VEP/84/cache --PLUGINS all
>
> and installs VEP as expected, when I ask it to download the cache files it
> fails at the end with
>
>  - downloading
> ftp://ftp.ensembl.org/pub/release-84/variation/VEP/xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz
> - unpacking xiphophorus_maculatus_vep_84_Xipmac4.4.2.tar.gz
> ERROR: For technical reasons this installer is unable to install GRCh37
> caches alongside others; please install them separately
>
> and I can't find any help as to what I should do next. For example,
> though, /gpfs/apps/VEP/84/cache/homo_sapiens has directories 84_GRCh37 and
> 84_GRCh38 which seem fully populated, though, so can this be safely ignored?
>
> If I then repeat the installation asking not to install any cache files
> and ask it to install all of the FASTA files the third one fails with
>
> ERROR: Could not change directory to dna
>
> and the installer then terminates, rather than trying the next one. I
> think this comes from lines 737 to 739 in INSTALL.pl:
>
>  foreach my $sub(split /\//, $3) {
>       $ftp->cwd($sub) or die "ERROR: Could not change directory to
> $sub\n$@\n";
>     }
>
> and suggests that there are some missing directories on the download site
> for these files. Is this the case and, if so, is there any way around this
> apart from rerunning the installer for each of the 70 options one-by-one,
> which would take quite a while?
>
> Apologies again if this is the wrong list and/or these are simplistic
> questions. Any help is much appreciated.
>
> Regards
>
> --
> Paul Hatton
> High Performance Computing and Visualisation Specialist
> IT Services, The University of Birmingham
> Ph: 0121-414-3994  Mob:07785 977340  Skype:P.S.Hatton
> [Service Manager, Birmingham Environment for Academic Research]
> [Also Technical Director, IBM Visual and Spatial Technology Centre]
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160419/41b18586/attachment.html>